Color Genetics 101-- The Base Color gene - "B"

All rabbits are either black or brown. Every other color is a variation of this basic color scheme. The "B" gene is responsible for producing the protein that causes a rabbit to be black or brown. The "B" gene comes in 2 forms (different forms of the same gene are called alleles) - B produces a black pigment and b produces a brown pigment.

Every rabbit has a pair of "B" genes. They can be the same or different. So genetically, a rabbit can be BB, Bb or bb.

A BB rabbit has only the B allele, so it is black.A bb rabbit has only the b allele, so it is brown (usually called chocolate).When a rabbit has BOTH alleles - Bb - it makes both types of pigments, but the darker black pigment 'covers up' the lighter brown pigment. So a Bb rabbit looks black.

Geneticists say black is dominant to brown or that the brown gene is recessive to black. Often we say the brown gene is hidden or you might hear a breeder say the brown gene is 'carried'. That's because if you breed two rabbits that are both carriers - Bb - they can recombine to give you an offspring that is bb (getting one of those brown alleles from each parent) and looks brown.

Note - geneticists use the capital letters for dominant alleles and the lowercase letters for the recessive alleles. Being consistent makes it easier to keep track -- you will always see the allele designated by the upper case letter if it is present but the allele designated by the lower case letter can be hidden.

Colors can vary quite a bit from breed to breed as well as due to the interactions between genes and other genes that modify the colors. Check out the differences between our black minirex and our black Jersey woolies on the "Colors in our Rabbitry" page. The long fur of the Jerseys tends to make the black color appear lighter.

-- The Dilution gene - "D"

The dilution gene cause a clumping of the pigment (if you look at hairs from a dilute rabbit under the microscope, you can see microscopic 'banding') which visually 'dilutes' the color we see (microscopic black and white lines look grey to the human eye). It also comes in 2 alleles - D produces full color and d produces a dilute color.

Every rabbit has a pair of "D" genes. They can be the same or different. So genetically, a rabbit can be DD, Dd or dd.

A DD rabbit has only the D allele - it is full color either black or chocolate.A dd rabbit has only the d allele - it is a diluted color. Dilute black is called blue and dilute chocolate is called lilac. When a rabbit has both alleles - Dd - the full color copy is still making enough of the regular pigment to 'cover up' the dilute. So a Dd rabbit looks full color (black or brown).

Colors can vary quite a bit from breed to breed as well as due to the interactions between genes. Check out the differences between our blue minirex and our blue Jersey woolies. The long fur of the Jerseys tends to make the black color appear lighter.

-- The Base Pattern gene - "A"

Ready to get a little more complicated?

The pattern gene affects not just the color itself but the where it appears on the rabbit. And it comes in not just two alleles, but three!

The three base pattern alleles are A which produces an agouti pattern, at which produces a tan pattern and a which produces the self (solid) pattern

Even though there are three alleles, each individual rabbit only has two genes - one from its mother and one from its father.

A rabbit which is aa has two copies of the self allele - so it will be a self (solid) colored rabbit in the color determined by the B and D genes.

A rabbit which is atat has two copies of the tan allele - so it will be a tan patterned rabbit. In a tan patterned rabbit the base color (determined by the B gene and modified by the D gene) shows over most of the rabbit, but the stomach, inside of the ears, rings around the eyes and underside of the cheeks are a light yellow-brown color (exact shades vary) called tan.

A rabbit which is AA has only the agouti allele - so it will be an agouti patterned rabbit. An agouti rabbit has all the tan pattern markings PLUS rings of the tan color all through its coat. (blow the coat gently to separate the fur in a circle - if you see rings, the rabbit is agouti!)

Agouti is the most dominant allele in this series. So rabbits which are Aat and Aa are also agouti patterned. Aat are agouti rabbits carrying tan. Aa are agouti rabbits carrying self.Tan is dominant over self so rabbits which are ata are tan patterned (carrying self).

Note: Geneticists call the sequence of genes I've been writing out - e.g., aabbDD - the rabbit's genotype. They refer to the color you actually see as the phenotype.

Let's look at the combinations so far as genotype(s) producing phenotypes:

These are starting to get to long to write all the genotypes. So I'm going to introduce a convention used by geneticists. You put a - in the genotype where there is more than one possibility. For example, A- means this can be AA, Aat OR Aa. Important to note the dashes are never used to indicate a more dominant gene -- dominant genes can't hide! For example, at- can be either atat or ata NOT atA. Tan can't hide agouti, the agouti shows!

Breeds also start diverging here on what they call certain colors. I'm including color names used in the following breeds - minirex (M), jersey wooly (J), American fuzzy lop (F) and angora (A).

-- The factory gene "C"

My own name for this gene, which most folks call 'color saturation" to use the "C" in its name. But I find that confusing since 'saturation' to me implies an effect of making a color lighter or darker whereas what this gene actually does is interfere with color production. And a lot of genetics websites speak of the alternate "C" alleles as 'stripping out' color - but they aren't really doing that either - the color just isn't being produced. Think of color in terms of a pigment being produced. At the base of each hair shaft, there's a little factory that produces color according to the recipe provided by the above 3 genes. The mutations (alleles) in the C series genes don't change the colors - they break the factory! Some alleles (c) result in a factory that doesn't work at all, while others cause a factory that just doesn't work as well.

The "C" series gene is where color genetics starts to get complicated - we have not 2 or 3 but at least 5 alleles possible for this gene (but remember, each rabbit only gets two of the 5) and some of them are co-dominant (meaning they interact rather than one covering the other.

Let's start with the two extremes - Our dominant C gene is the one that produces all the nice normal colors above. The recessive c is the one that breaks the whole factory. So long as a rabbit has at least one C gene, its color 'factory' works normally. If the rabbit has two c alleles (cc) the whole pigment factory breaks down and you have an albino rabbit - white with red eyes.

C- = normal colorscc = red-eyed white (REW)

No matter what color the "A" "B" and "D" genes (as well as "E" below) say the rabbit should be, the cc genotype gives you a broken factory. The 'recipe' is still intact so the REW rabbit still carries whatever color(s) it would have been (or carried) had it gotten a normal C allele. Mate a REW back to a rabbit that will give the kits a normal C allele and all those hidden colors can come back.

The chinchilla allele (chd) - gives you a factory that can still make base pigments (black/brown/blue/lilac) pigments but can't make tan (yellow/orange/red). So all the parts of the rabbit that would normally appear those colors are now silver-white. C is dominant to chd -- if you've got one copy of the C gene, you are still going to make all those nice tan pigments. chd is dominant to REW but the chd version of the factory is a little bit weak. If you have only one chd allele, you still get the black pigment, but it might not be a clear as you would like.

So what colors does that give you?

On a self rabbit, there weren't any tan pigments to begin with. So you get all your normal self colors - but they are chinchilla carriers (and called self-chins).

On a tan pattern rabbit, all the normal tan markings are replaced with silver white. This color pattern is called silver marten - silver martens come in black, blue, chocolate and lilac, just as you might expect.

On an agouti rabbit, all the tan markings, including the rings, are replaced with the silver-white. This color pattern is called chinchilla. Chinchillas also come in black, blue, chocolate and lilac. Some breeds give different names to these colors - for example in Jersey woolys, blue chinchilla is called squirrel. Some breeds don't accept certain colors - that doesn't mean they don't exist, just that they can't be shown.

The next allele in the series is formally referred to as the 'light chin' allele (chl) but more commonly the shaded allele. The factory made by the chl allele is broken, but in a different way than the chd or c alleles. Like the chd allele, this factory can't produce tan pigments at all. In making the black pigments, this factory works perfectly fine on the head, ears and feet, but gradually stops working towards the back (saddle) of the rabbit. The gene is temperature sensitive, with the warmer parts of the rabbit (body) showing the least color. Temperature at the time of the molt can affect color on shaded rabbits - chilled kits can be very dark, rabbits that molt during warm weather can be much lighter. The effect is not a dilution (which would make the black pigment more grey) but causes a color shift in which the black pigments take on a warmer 'sepia' tone before fading out. Interestingly, the chl allele does not seem to work the same way on the chocolate version of eumelanin as it does on the black. In my personal experience, genetic shaded chocolates (bb chl-) show little to no shading, but the eye color shifts to a pale gold with an extreme ruby cast.

C is almost completely dominant over chl - so long as you have one good factory, everything is working fine. The ‘almost’ comes into play with the eye color. Rabbits which are shaded carriers (Cchl) often have a ruby cast to their eyes.

Chd is not completely dominant over chl. Chinchilla rabbits carrying the shaded allele (A-chdchl) MAY look like normal chins or they may look somewhere in between chin and shaded (shaded agouti). Chinchilla rabbits carrying shaded will usually have the ruby cast to their eyes. Self chin rabbits carrying the shaded allele (aachdchl) are usually going to look like self, but they may lighten to seal (below) and may also have the ruby cast to their eyes.

If the rabbit has two copies of the chl allele (chlchl) they compensate for one another and manage to produce most of the color. Self rabbits with two chl alleles (aachlchl) rabbits are called seals and their color can range from nearly black to more of a brown-black shade (like the aquatic mammal for which the color is named – sometimes referred to as a sepia tone – like the old-fashioned photos). Seals also come in blue seal (blue grey with a sepia tone, chocolate seal and lilac seal). You can almost always tell a seal from a self by looking at the hocks (bottom of the feet) – the sepia tone of the seal color is most apparent there (no idea if you can do that when the base color is already chocolate/lilac). Seals may also have the ruby cast to their eyes. Tan pattern rabbits with two chl alleles (at-chlchl) are called seal martens. Seal martens pretty much look like silver martens, but their base color is going to also have the sepia tone and their eyes may have the ruby cast. I haven’t been able to find any information about agouti seals (A-chlchl) – if anyone knows, please drop me a line! My expectation based on how the seal allele works is that a seal agouti would look like a chinchilla, with a seal tone to its black bands and ruby cast to the eyes.

A self rabbit with only one copy of the chl allele (and no C or chd to compensate – so chlch or chlc) has a much harder time making enough pigment. These rabbits are called sables (or sometimes just shaded). The head, ears and feet come out the normal base color with a strong sepia tone, but the black-base color fades (shades) to a lighter color (often near white) over the back. Blue-based sables also pick up a sepia tone (called smoke in many breeds) and fade to a lighter color over the back. Interestingly, the chocolate- and lilac- base colors don't seem to shade the same way -- the coat of a chocolate sable is almost the same intensity as a regular chocolate, and the 'sepia tone' is invisible against the already warm tone of a chocolate base. I've owned 3 rabbits to date with a bb chl- genotype (1 chocolate sable, 1 chocolate seal and 1 chocolate chin). All three had very striking and unusual color eyes -- a very pale gold with an incredibly strong ruby cast. Thus genetic sables come in all base colors – black (Siamese sable), blue (smoke pearl), chocolate (chocolate sable) and lilac (lilac sable), but chocolate sables and lilac sables do not show defined 'shading' and are not showable in any breed. Shaded acts pretty much the same when combined with the tan pattern allele, except that you add the silver-white marten markings to get sable martens. Shaded agoutis are often pejoratively referred to as ‘shagouti’ and one of the 'first rules' of color breeding is the caution that you should never mix shaded alleles with agoutis! (apparently unshowable in any breed). I've now raised both a sable chin and a chocolate sable chin (in French angora). At birth, the former was a color 'in between' chocolate and blue; as she aged, Quicksilver developed a coloring intermediate between a sable and a chinchilla -- clear chinchilla rings on the face, rings with the distinctive 'sepia tone' on the shoulders and hindquarters, and a near white saddle. Milkshake, the chocolate sable chin, looked chocolate at birth and nearly chocolate chin at adulthood, with just a minor fading/blurring of rings in the saddle, but the strangest eye color (pale grey-gold with a very strong ruby cast).

The next allele in the series is called pointed and designated ch. The ch gene makes a version of the ‘pigment factory’ that cannot make the tan pigments at all and in which production of the base pigment is temperature sensitive! The pointed allele is recessive to C, chd and chl. If you have one of those alleles, you have a factory enough better than the pointed version to cover pointed.

The ch version of the factory makes normal base pigments on the portions of the rabbit that are colder – that is, on the points – ears, nose, feet and tail. On the warmer portions of the rabbit, the factory shuts down leaving the rabbit white. Interestingly, pointed kits that get chilled following birth and pointed rabbits that go through a molt while exposed to cold weather often develop ‘smut’ – black markings on the portions of the coat that ‘should’ be white. Conversely, kits exposed to heat (summer litters) and pointed rabbits molting during hot weather fail to develop good color on their points.

The pointed allele is almost completely dominant over the albino (REW) allele. Most breeders specializing in pointed rabbits say that the chc genotype doesn’t produce as good markings. For the casual breeder, this is probably less a factor than temperature!

Showable pointed rabbits are selfs (aach-). Presence of the tan allele (at-ch-) makes the inside of the ears go white (otter himis). Presence of the agouti allele (A-ch-) also causes the insides of the ears to go white AND adds silver-white banding in the fur of the points!

-- Extension gene "E"

With me so far? Ready to get even more complicated?

The extension series gene works on the balance between the black/brown pigment in a rabbit and the yellow/red (tan) pigment. It is best known for producing reds and torts, but it actually has at least 4 alleles! The expression of the "E" genes depends on how they are combined with the "A" pattern genes.

A and E work together like a lock and key. They are opposites in the sense that the more dominant A genes tend to make the rabbit more red while the dominant E genes make the rabbit more black. A-ee makes red (or orange/fawn/tan/cream) rabbits, aaE- makes black (or blue/chocolate/lilac). The combination can also be temperature sensitive -- with a tendency to favor black towards the points (and in colder conditions).

Let's start with the basic two...E (full extension) is dominant over e (non-extension or 'light' extension). EE or Ee produces the normal extension colors we've talked about so far. ee can be thought of as extending the light (red/tan) color.

Not an exact match to the biochemistry, but I find it helps to think of it this way... A is a key, E is a lock. When both are working, you can turn the switch to make the color shift back and forth - black-red-black to get the normal banding of the agouti coat. With the aa genotype, your key is broken - it sticks in the normal lock so you get only black pigment. With ee, the lock is broken -- and is temperature sensitive. When it is warm, the key doesn't fit at all and you make red pigment. When it is cold, the key sort of fits and you can make a little black pigment (smut on the ear tips being the most common) but the key tends to fall out, switching you to red pigment. So what happens when both the lock AND key are broken (aaee)? In the cold, the broken key fits - and gets stuck in the 'black' position. In the warm, the broken key doesn't fit and you get red. A-E- = agoutis aaE- = selfsA-ee = reds (including oranges, fawns and creams)aaee = torts

So what about at? The A-gene is still coding for the key -- the at version is just broken 'in a different way'. The at 'key' doesn't switch correctly either, but it tends to get stuck in its 'initial position' So everywhere that normally starts black (e.g., black tipping on agouti) the key gets stuck in the 'black' mode. But the places that don't have tipping (e.g., belly, triangle, inside ears, jawmarks, etc) the key doesn't fit and you stay in the 'red/tan' mode.

at-E- = tans (otters and martens)

And when this 'differently broken' key combines with our broken lock (at-ee)? Then the temperature sensitivity of ee comes into play. Anywhere the coat starts red, the 'at key' still gets stuck in 'red mode' and you get red agouti marks. Anywhere warm, the key doesn't fit and the coat is red. But when cold, this 'at key' fits better than the A- version -- the key doesn't fall out easily and you get quite a lot of the black pigment. Combined with the tan pattern gene, the e gene produces a color series known as fox or 'tort otter'. ARBA doesn't recognize fox (so it can't be shown) though other countries do. Foxes have all the traditional agouti marks (eye circles, pale belly) and are mostly red, but the body shades to darker faces, feet and tails rather like a tort. Occassionally foxes will 'pass' for a smutty orange, particularly when warm temperatures are in play, limiting the black pigment.

at-ee = foxes

Next...

Es is said to be the most dominant of the "E" series, but actually express a degree of co-dominance (within the pair, the alleles interact rather than one covering the other) in addition to interacting with the pattern gene. This is another 'broken switch' in which the A-key sticks, allowing red color to be produced only very briefly resulting in red/tan color being possible only near the tip of guard hairs. Es is dominant over both E and e, but co-dominant with itself.

Though not biochemically accurate, some refer to this allele as extending the dark color or 'pushing' the midband to the tip. It is a useful mnemonic for remembering how this gene acts. Combined with agouti, the Es gene extends the dark pigment farther up the shaft (making the mid band appear dark like the undercoat) and pushing the segment that was the mid-band (tan color) to the tip - these are called gold-tipped steels. The classic steel (silver-white tipping, aka silver tipped steel) is achieved by adding a chinchilla gene (chd) to 'bleach' the tips. Interestingly, in rabbits that are EsEs (getting the steel gene from both parents) the undercoat color is pushed all the way to the tip - giving a rabbit that appears self even though genetically it is agouti.

Steel is usually kept away from tan lines -- in theory a 'steel tan' or 'steel marten' would result in a rabbit that shows the steel ticking only in the tan portions of the coat - eye circles, jowls, belly, etc. But I haven't been able to find a clear record of this.

With me so far?

Our next allele is ej, ej creates a lock that is broken VERY differently. Harlequin is a fragile gene -- very early in the development of the rabbit, in some cells this gene breaks completely and the entire switching mechanism is lost -- cells descended from this line lose all ability to make black pigments. In other cells, the switching mechanism survives, but is stuck in the 'black' mode - regardless of what key you try to put in.

ejej = Solid patches of black and red. The arrangement of those patches depends on other genes that control the migration of cells during development. The ideal 'harlequin' pattern or alternating patches depends on several developmental genes getting those patches in the right locations.

Because ej acts differently in the two cell lines, it interacts with Es, E and e differently in each of those lines. In the patches where the switching mechanism is missing, the other gene compensates completely -- in those cells, Esej acts like Es-, Eej acts like E- and eje acts like ee. In the patches where ej creates a broken switch, it is dominant, always producing full black pigment.

A-Esej - patches of black (ej) and patches of steel (appear A-Es-) - very darkat-Esej - patches of black (ej) and patches of steel-tan? (appear at-Es-) - very darkaaEsej - blackA-Eej - patches of black (ej) and patches of agouti (appear A-E-) - very darkat-Eej - patches of black (ej) and patches of tan pattern (appear at-E-) which look orange only where they cross the orange markings of a tan pattern - very dark, unable to produce good harlequin patchingaaEej - black A-eje - patches of black (ej) and patches of red (appear A-ee) - potentially a good harlequinat-eje - patches of black (ej) and patches where tort otter pattern shows through (appear at-ee) - this will never produce the face split of a good harlequin as both halves of the face are black.aa-eje - patches of black (ej) and patches where tort pattern shows through (appear aaee) - this will never produce the face split of a good harlequin as both halves of the face are black.A caution in working with the E series! As if it weren't complicated enough, several additional genes are needed in order to produce good color and pattern in this group. Rufus factor (see below) shifts the chestnut shade of the normal agouti bands towards red. Wideband (W series) doubles the width of the agouti midband which can be important in some breeds for distinguishing red, orange and copper and in other breeds are considered essential for proper color. Other genes appear to control 'smut' (an undesirable black tipping in the orange/red portions of the fur). Still others are critical to the distribution, shape and size of the patches in a harlequin.

The Broken gene – “En”

Let me start by saying I really hate the fact that we are reusing the letter E for this gene. I know that’s the standard symbol, and it is short for 'English spotting' but this isn’t on the “E” series like the letter might lead you to think! And even though it also produces white patterns and interferes with the ‘factory’, it isn’t on the “C” series either. No, it’s a totally separate gene. Here’s my analogy – the “C” series gene makes the factory but the broken gene makes a monkey wrench that gets tossed in and breaks the factory. I like the monkey wrench analogy because the way the gene works is to shut down factories in patches. At some point early in development (which is why you get patches rather than speckling) the broken allele produces a protein (our monkey wrench) that gets tossed at the factory. Sometimes it misses, creating a colored patch, and sometimes it hits, breaking the factory completely and creating a white patch.

The broken gene has two alleles, broken (En) and normal (en) - normal isn’t making any monkey wrenches, so no factories get broken and all the color comes through. These genes are co-dominant – if you have two En genes you get twice as many monkey wrenches!

EnEn produces a rabbit that has more than 90% white this is called a Charlie.

Enen produces a broken rabbit between 10% and 90% white.

enen produces the normal colored rabbit without white patches.

The broken allele cannot be carried by colored rabbits. If the gene is there, you will see the white patches. The exception is rabbits that already have a lot of white in their ‘normal’ colors. Red-eyed whites (REW) and pointed rabbits are already really white, so the white patches against the white coat likely won’t show up – meaning REWs and himis can carry broken (if all the factories are already out of commission, throwing monkey wrenches doesn’t change anything!).

The Vienna Gene (V)

This is another gene that causes white color – but is completely separate from the “C” series and broken genes. The Vienna gene has two alleles – V produces normal color and v breaks the factories. The v allele is almost completely recessive to the V allele. So unlike the broken gene, you need two copies of the v allele to make a good monkey wrench – but when you do it is a really, really good wrench! If you have two copies of the Vienna allele (vv) all the factories responsible for the fur color break and the rabbit will be white. Interestingly, the factories responsible for the eye color still produce a dilute pigment resulting in blue eyes - a very bright blue color quite distinct from the 'blue-grey' eyes common to the dd genotype rabbits. Thus Vienna rabbits (vv) are also referred to as blue-eyed whites(BEW). Like REW’s, BEW’s can hide any color or pattern – the ‘recipe’ genes ABDE are all there and will be passed to the offspring. Like REW’s BEW can also hide broken. Since Vienna is on a separate gene, BEW (unlike REW) can also hide chinchilla, shaded and himi. It can hide a REW carrier genotype (Cc, chdc, chlc, chc) but can’t hide REW (cc) as the two cc alleles still result in a factory that doesn’t work at all (ccvv = REW).

VV rabbits, as you’ve probably figured out, have all the normal colors.

The Vv genotype results in normal colored rabbits that hide the Vienna allele (Vienna carriers) and often in rabbits with stray white marks (Vienna marked rabbits). The number and placement of vienna marks are controlled by other genes, but often mimic the pattern of dutch rabbits, with the white blaze being common. If a vienna mark falls across the eyes, that eye (or portion of an eye) will be blue.

The Wideband gene “W”

The wideband gene is not discussed often and when it is, it is often confused with the nonextension gene (e), probably because it has a similar effect and the two are usually ‘used’ together.

The wideband gene has two alleles. W is dominant, so Ww and WW both produce the normal colors. The ww genotype doubles the width of the ‘red’ bands in agouti rabbits.

The wideband allele is most common in non-extension rabbits (reds - A-eeww and torts aaeeww), where it helps to reduce smut and intensify the red color. It is also common in coppers - along with high rufus factor it helps to distinguish the copper from the chestnut agouti.

In chinchilla rabbits (A-chd-ww), the wideband gene doubles the width of the silver-white bands, resulting in rabbits that are lighter and less even than normal. In other agouti rabbits (A---ww) the bands are also wider and the red shade may be more intense as well. In general, wideband is accepted but not preferred in the chinchilla and other agoutis. Since the selfs and tans don’t have bands, the wideband effect is not seen, and is just carried.

Silver (si)

The silver gene is a recessive allele which bleaches the guard hairs - as seen in silver and silver fox rabbits. Rabbits which show silvering are sisi - those which don't are SiSi (usually) or Sisi.

The rufus factors

Rufus factor is not a single gene, but a whole series of genes acting together to intensify/lighten the amount of red found in the tan pattern and bands. I find it helpful to think of this as a series of 5 genes each with two alleles + (for redder) and – (for yellower). The reddest possible rabbit then gets 10 + alleles (5 pairs) and the lightest 10 – alleles. A rabbit with 5 + and 5 – will be somewhere in between (whether that’s +-+-+-+-+- or +++++-----). If someone out there know more about how this actually works, please let me know! I’d much rather do this properly!